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- PDB-4n8q: Alternative substrates of Mycobacterium tuberculosis anthranilate... -

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Basic information

Entry
Database: PDB / ID: 4n8q
TitleAlternative substrates of Mycobacterium tuberculosis anthranilate phosphoribosyl transferase
ComponentsAnthranilate phosphoribosyltransferase
KeywordsTRANSFERASE / Anthranilate Phosphoribosyltransferase / Anthranilic Acids / Magnesium / Tryptophan / Inhibitor / Magnesium binding Phosphoribosyl pyrophosphate
Function / homology
Function and homology information


anthranilate phosphoribosyltransferase / anthranilate phosphoribosyltransferase activity / tryptophan biosynthetic process / magnesium ion binding / extracellular region / plasma membrane / cytosol
Similarity search - Function
Anthranilate phosphoribosyl transferase / Transferase, Pyrimidine Nucleoside Phosphorylase; Chain C / Pyrimidine Nucleoside Phosphorylase; Chain A, domain 2 / Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain / Transferase, Pyrimidine Nucleoside Phosphorylase; Chain A, domain 3 / Glycosyl transferase family 3, N-terminal domain / Glycosyl transferase family 3, N-terminal domain superfamily / Glycosyl transferase family, helical bundle domain / Glycosyl transferase, family 3 / Glycosyl transferase family, a/b domain ...Anthranilate phosphoribosyl transferase / Transferase, Pyrimidine Nucleoside Phosphorylase; Chain C / Pyrimidine Nucleoside Phosphorylase; Chain A, domain 2 / Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain / Transferase, Pyrimidine Nucleoside Phosphorylase; Chain A, domain 3 / Glycosyl transferase family 3, N-terminal domain / Glycosyl transferase family 3, N-terminal domain superfamily / Glycosyl transferase family, helical bundle domain / Glycosyl transferase, family 3 / Glycosyl transferase family, a/b domain / Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain superfamily / Up-down Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
2-amino-4-fluorobenzoic acid / Anthranilate phosphoribosyltransferase / Anthranilate phosphoribosyltransferase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.08 Å
AuthorsCastell, A. / Cookson, T.V.M. / Bulloch, E. / Evans, G.L. / Baker, E.N. / Lott, J.S. / Parker, E.J.
CitationJournal: Biochem.J. / Year: 2014
Title: Alternative substrates reveal catalytic cycle and key binding events in the reaction catalysed by anthranilate phosphoribosyltransferase from Mycobacterium tuberculosis.
Authors: Cookson, T.V. / Castell, A. / Bulloch, E.M. / Evans, G.L. / Short, F.L. / Baker, E.N. / Lott, J.S. / Parker, E.J.
History
DepositionOct 17, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 23, 2014Provider: repository / Type: Initial release
Revision 1.1May 21, 2014Group: Database references
Revision 1.2Jul 2, 2014Group: Database references
Revision 1.3Dec 17, 2014Group: Data collection
Revision 1.4Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Anthranilate phosphoribosyltransferase
B: Anthranilate phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,8924
Polymers77,5822
Non-polymers3102
Water5,296294
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1720 Å2
ΔGint-19 kcal/mol
Surface area26200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.587, 90.998, 120.039
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Detailsbiological unit is the same as asym.

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Components

#1: Protein Anthranilate phosphoribosyltransferase


Mass: 38790.848 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: MT2248, MTCY190.03c, Rv2192c, trpD / Plasmid: pET23a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P66992, UniProt: P9WFX5*PLUS, anthranilate phosphoribosyltransferase
#2: Chemical ChemComp-FA0 / 2-amino-4-fluorobenzoic acid


Mass: 155.126 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H6FNO2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 294 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.8 Å3/Da / Density % sol: 56.09 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1 M imidazole/malate, 7.5% PEG4000, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95365 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 13, 2010
RadiationMonochromator: Silicon double crystal Reflections / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95365 Å / Relative weight: 1
ReflectionResolution: 2.08→120.039 Å / Num. all: 52823 / Num. obs: 52823 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.2 % / Biso Wilson estimate: 33.7 Å2 / Rmerge(I) obs: 0.077 / Rsym value: 0.077 / Net I/σ(I): 17.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.08-2.27.40.4821.55585875860.482100
2.2-2.337.40.3222.35320772320.322100
2.33-2.497.30.2283.24981167800.228100
2.49-2.697.30.1594.64644163390.159100
2.69-2.957.30.1126.64268358550.112100
2.95-3.37.20.0759.33803352820.075100
3.3-3.870.054123329347380.054100
3.8-4.666.90.04514.12764640130.045100
4.66-6.596.90.04214.82165831580.042100
6.59-120.0396.70.03315.81226518400.03399.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.15data scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
DNAdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3QR9

3qr9


Resolution: 2.08→72.52 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.925 / WRfactor Rfree: 0.233 / WRfactor Rwork: 0.195 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8688 / SU B: 4.262 / SU ML: 0.115 / SU R Cruickshank DPI: 0.181 / SU Rfree: 0.1626 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 4.1 / ESU R: 0.181 / ESU R Free: 0.163 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2344 2667 5.1 %RANDOM
Rwork0.1973 ---
all0.48 52823 --
obs0.1991 52750 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 69.6 Å2 / Biso mean: 33.6265 Å2 / Biso min: 14.59 Å2
Baniso -1Baniso -2Baniso -3
1--2.2 Å2-0 Å20 Å2
2--2.21 Å2-0 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.08→72.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5004 0 22 294 5320
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0225165
X-RAY DIFFRACTIONr_angle_refined_deg1.4761.9527053
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8755698
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.94422.367207
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.66915735
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3431554
X-RAY DIFFRACTIONr_chiral_restr0.0980.2816
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214006
X-RAY DIFFRACTIONr_mcbond_it0.9711.53439
X-RAY DIFFRACTIONr_mcangle_it1.75525448
X-RAY DIFFRACTIONr_scbond_it2.5631726
X-RAY DIFFRACTIONr_scangle_it4.1874.51603
LS refinement shellResolution: 2.084→2.138 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.287 197 -
Rwork0.233 3639 -
all-3836 -
obs-55858 99.79 %

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